Friday, March 7, 2008

Equivalent competence phenotypes?

I am working on the Discussion of our competence manuscript and am trying to think about whether all DNA uptake phenotypes might be functionally equivalent. This means that cells are equally happy if they each take up 100 molecules or only one molecule. Given what we know about competence I don't think that this is the case but we evolutionists like to consider neutral explanations along with selective ones. So here is the paragraph:

"An additional ultimate cause of variation in competence is that the majority of the variation is functionally neutral. This would be the case if has been beneficial for cells to take up some DNA with the precise quantity being unimportant. Under this scenario, the high DNA uptake phenotype of strain Rd would be functionally equivalent to the low DNA uptake phenotype of strain Eagan. If we assume that all cells in a culture are competent then in our assays each Rd cell took up an average of 89 molecules of donor DNA whereas in Eagan each cell took up only one molecule of DNA. Each double-stranded donor molecule was 444 nucleotides (222 bp) so Rd and Eagan would have taken up 444 x 44 = 19,536 and 444 x 1 = 444 nucleotides, respectively. Considering the genome sizes of these bacteria are greater than 3.6 x 10^9 nucleotides (1.8 Mb), the DNA taken up by both strains would contribute little to whole genome replication. However, DNA is taken up by most strains when replication is needed for DNA repair and not whole chromosome copying. Depending on the extent to which cells need to use DNA replication during repair, every nucleotide taken up may help so the differences in competence between strains are likely to have a strong influence on the function of competence."

I am trying to think of obvious flaws in this reasoning. I am sure they are there but my brain is tired today.

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